The isolation of RNA from biological samples is called RNA extraction. Such extraction from cellular material is complicated by the ubiquitous presence of ribonuclease enzymes in cells and tissues, which can rapidly degrade RNA. Methods commonly used in molecular biology to purify RNA from biological samples include guanidinium thiocyanate-phenol-chloroform extraction (phenol-chloroform extraction) and RNA extraction in liquid nitrogen.
The liquid-liquid extraction technique of phenol-chloroform extraction is widely used in molecular biology for purification of RNA. This method includes forming a biphasic mixture of equal volumes of a phenol:chloroform mixture and an aqueous sample. The method relies on phase separation by centrifugation of the phenol:chloroform mixture and the aqueous sample resulting in an upper aqueous phase and a lower organic phase. Extraneous cellular proteins partition in the organic phase while RNA partitions in the aqueous phase. RNA is subsequently recovered from the aqueous phase by precipitation with ethanol or 2-propanol. A disadvantage to phenol-chloroform extraction is that both phenol and chloroform are hazardous and inconvenient to use. Further, the extraction process is often laborious.
More difficulty lies in providing an extraction procedure that isolates RNA quickly in the presence of clays, phyllosilicates, or metal ions within the sample mixture. Most RNA isolation methods which remove metal ions from samples prior to extraction require lengthy wash steps prior to cell lysis which is undesirable for those who desire to perform metatranscriptomic and RNA analysis experiments.
The rapid isolation of RNA in the presence of metal cations is desirable as these cations can bind irreversibly causing RNA degradation. Additionally, through biosorption, living and non-living bacterial cells can pre-concentrate aqueous solutions of metal cations due to adsorption of metal ions to the chemical functional groups on the cell surface.
Thus, improvements in methods and systems for isolating RNA from bacterial samples exposed to clay mixtures, clay minerals, silicate minerals, including phyllosilicates, and aqueous solutions including metal cations are desirable.